Contacts of the strand formed by residues 75 - 89 (chain E) in PDB entry 3M4D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 75 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70E GLU* 3.7 4.7 - - - +
71E GLU* 3.1 58.8 + - + +
72E GLY 4.8 0.3 - - - +
73E ALA 3.5 1.2 - - - -
74E ASN* 1.3 90.9 + - + +
76E SER* 1.3 64.5 + - - +
206E ALA* 3.6 2.4 - - - +
258E LEU 3.4 4.9 - - - +
259E HIS* 3.5 21.8 - - + -
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Residues in contact with SER 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E VAL* 3.1 18.7 - - - +
69E SER 2.9 21.0 + - - -
70E GLU* 4.3 3.4 - - - +
75E LYS* 1.3 76.6 - - - +
77E GLY* 1.3 58.4 + - - +
206E ALA* 3.5 19.5 - - - -
207E ALA* 3.5 16.0 - - - +
210E PHE* 3.4 10.9 - - - -
257E GLN* 3.4 6.7 - - - +
258E LEU 3.0 31.6 + - - +
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Residues in contact with GLY 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E VAL* 3.1 9.5 - - - +
68E TYR* 2.9 49.6 + - - -
69E SER* 3.0 11.5 + - - -
76E SER* 1.3 75.1 + - - +
78E LEU* 1.3 59.2 + - - -
210E PHE* 4.0 3.1 - - - -
255E ASP* 4.2 0.9 - - - -
256E TYR 3.5 5.6 - - - -
257E GLN* 4.3 4.3 - - - -
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Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E TYR* 3.6 44.2 - - + +
66E ARG* 3.3 37.5 - - - +
67E VAL* 3.6 4.5 - - + +
68E TYR* 3.4 3.9 - - - -
77E GLY* 1.3 73.1 - - - +
79E ALA* 1.3 63.2 + - - +
80E TRP* 3.9 2.7 + - + -
196E PHE* 3.7 28.3 - - + -
210E PHE* 3.7 27.8 - - + -
254E ASP 3.6 2.3 - - - +
255E ASP* 3.6 1.6 - - - -
256E TYR* 2.7 44.4 + - + +
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Residues in contact with ALA 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLN 3.4 6.4 - - - +
65E TYR* 3.3 3.3 - - - -
66E ARG* 2.8 41.0 + - + +
68E TYR* 3.7 12.6 - - + -
78E LEU* 1.3 74.0 - - - +
80E TRP* 1.3 61.2 + - - +
253E ARG* 3.8 22.2 - - - +
254E ASP 3.5 5.6 - - - -
274E TRP* 3.7 23.8 - - + -
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Residues in contact with TRP 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLN 4.9 0.4 - - - -
65E TYR* 4.0 19.3 - - + +
78E LEU* 3.9 12.3 - - + -
79E ALA* 1.3 74.9 - - - +
81E PRO* 1.3 94.6 - - + +
82E SER* 3.3 8.1 + - - -
171E PHE* 3.5 36.8 - + - -
184E ARG* 3.7 23.6 - - + -
195E LEU* 3.7 17.3 - - + -
196E PHE* 3.4 23.8 - + + -
220E LEU* 3.5 10.8 - - + -
253E ARG* 3.1 8.2 - - - +
254E ASP* 2.8 62.5 + - + +
256E TYR* 3.9 6.8 - - + +
269E ASN* 3.0 25.8 + - - -
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Residues in contact with PRO 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E GLY 3.5 18.6 - - - +
65E TYR 4.4 1.1 - - - +
80E TRP* 1.3 95.9 - - + +
82E SER* 1.3 62.7 + - - +
83E ALA 3.3 1.7 + - - +
84E PHE* 3.6 30.3 - - + -
153E PHE* 3.8 8.8 - - - -
220E LEU* 3.3 49.5 - - + +
251E ARG* 4.1 9.9 - - + -
252E VAL 3.5 7.2 - - - +
253E ARG* 4.3 2.7 - - + -
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Residues in contact with SER 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E TRP* 3.3 18.7 + - - -
81E PRO* 1.3 72.6 - - - +
83E ALA* 1.3 63.6 + - - +
153E PHE* 4.7 0.9 - - - -
170E ILE* 3.5 2.8 - - - +
171E PHE* 2.9 27.2 + - - +
184E ARG* 3.7 18.8 + - - -
252E VAL* 2.9 24.6 + - - +
254E ASP* 2.8 38.7 + - - -
272E ASP* 3.9 0.3 + - - -
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Residues in contact with ALA 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E PRO 3.3 1.8 - - - -
82E SER* 1.3 83.8 - - - +
84E PHE* 1.3 66.9 + - - +
85E LYS* 4.3 12.5 + - - -
153E PHE* 5.0 0.2 - - - -
169E VAL 3.4 6.5 - - - -
170E ILE* 4.0 18.4 - - + -
251E ARG* 3.4 6.1 - - - +
252E VAL* 2.8 51.7 + - + +
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Residues in contact with PHE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ILE* 3.5 47.3 - - + -
62E ALA 3.9 7.0 - - - -
63E GLY* 4.1 0.4 - - - -
81E PRO* 3.6 24.7 - - + -
83E ALA* 1.3 76.8 - - - +
85E LYS* 1.3 62.7 + - - +
86E VAL* 5.9 0.2 - - - -
153E PHE* 3.9 24.2 - + - -
167E TRP 4.6 0.2 - - - -
168E LYS* 3.3 3.5 - - - -
169E VAL* 2.8 46.9 + - + +
219E LEU* 3.3 29.6 - - + -
224E PHE* 3.7 40.6 - + + -
250E GLU 3.5 4.0 - - - +
251E ARG* 4.6 2.9 - - + -
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Residues in contact with LYS 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ILE* 4.0 2.3 - - - +
83E ALA* 4.3 11.2 - - + -
84E PHE* 1.3 83.6 - - - +
86E VAL* 1.3 69.1 + - - +
87E GLN* 4.3 21.7 - - + +
158E GLU* 4.4 8.0 + - - +
167E TRP 3.3 8.5 - - - +
168E LYS* 3.9 24.2 - - + +
170E ILE* 5.8 0.2 - - - -
228E PHE* 6.1 0.7 - - - -
248E ILE 4.2 1.1 - - - -
249E TYR* 3.4 1.4 - - - -
250E GLU* 2.9 62.4 + - + +
252E VAL* 4.0 20.9 - - + +
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E THR* 3.5 28.5 - - + +
61E ILE* 4.6 2.2 - - + -
85E LYS* 1.3 80.2 - - - +
87E GLN* 1.3 66.8 + - - +
88E LEU* 4.5 8.1 - - + -
166E GLY* 3.1 2.8 - - - -
167E TRP* 2.9 31.9 + - + -
224E PHE* 5.6 1.1 - - + -
226E PRO* 3.7 31.0 - - + -
228E PHE* 3.8 20.6 - - + -
247E VAL* 4.8 0.4 - - + -
248E ILE 3.3 4.5 - - - +
249E TYR* 3.8 28.5 - - + -
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Residues in contact with GLN 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E LYS* 4.3 25.1 - - + +
86E VAL* 1.3 84.2 - - - +
88E LEU* 1.3 67.2 + - - +
89E GLN* 6.2 0.7 - - + -
158E GLU* 4.3 11.5 + - - +
165E VAL 3.4 9.2 - - - +
166E GLY* 4.4 6.5 - - - -
167E TRP 5.1 0.9 - - - +
246E ASP 3.7 0.6 - - - +
247E VAL* 3.3 5.5 - - - +
248E ILE* 2.8 58.0 + - + +
250E GLU* 4.7 9.8 + - + +
277E ARG* 5.4 3.5 + - - -
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Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ILE* 4.0 26.7 - - + -
57E THR* 4.2 15.3 - - + -
86E VAL* 4.5 3.1 - - + -
87E GLN* 1.3 83.5 - - - +
89E GLN* 1.3 62.3 + - - +
98E ILE* 4.4 2.6 - - + +
164E LYS* 3.4 4.4 - - - +
165E VAL* 2.9 42.1 + - + +
167E TRP* 3.8 20.4 - - + -
230E THR* 3.5 31.2 - - + +
245E ILE* 4.0 22.7 - - + -
246E ASP 3.3 5.2 - - - +
247E VAL* 4.2 14.8 - - + -
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Residues in contact with GLN 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E GLN* 6.2 0.4 - - + -
88E LEU* 1.3 77.5 - - - +
90E LEU* 1.3 72.8 + - - +
91E PRO* 3.9 2.8 - - + +
92E ASP* 5.3 4.2 - - - +
163E LYS* 3.4 8.5 - - + +
164E LYS* 4.2 29.2 + - + +
245E ILE* 3.5 7.3 - - - +
246E ASP* 2.9 50.3 + - + +
248E ILE* 5.0 11.3 - - + +
277E ARG* 5.8 2.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il